Bioengineering cotton fiber properties

ABSTRACT

The present invention provides plant fiber expansion (FE) genes that encode FE polypeptides, such as phosphoenol pyruvate carboxylase (PEPcase), expansin, endoglucanase, xyloglucan endoglycosyltransferase (XET), and pectin methyl esterase (PME). The invention further provides fiber-specific promoters. Still further, the invention provides molecular strategies for modulating fiber quality in fiber producing plants by modulating expression of FE genes or mutant forms of FE genes.

FIELD OF THE INVENTION

[0001] The present invention is directed to plant genetic engineering. In particular, it relates to the isolation of nucleic acid molecules that modulate fiber quality, and the use of these nucleic acid molecules to produce transgenic plants with varied cotton fiber characteristics and quality.

BACKGROUND OF THE INVENTION

[0002] Cotton is a widely used textile fiber. For example, cotton textiles are used for clothing, home furnishings, blanket fills, toiletry products, industrial garments, etc. The expansive utility of cotton textile products is attributed to the relative ease of cotton production compared to other fibers and their appealing properties. As clothing, cotton fabrics are comfortable to wear because they are soft and breathable. Furthermore, cotton fibers are highly absorptive and possess good wicking properties, thereby allowing the use of the fibers in absorbent articles.

[0003] Although cotton is one of the most popular textile fibers used, it has many disadvantages. For example, cotton fabrics become worn out readily after several cycles of laundering. This is because, cotton fibers break or pill due to mechanical agitation during wash and form a lint on the surface of the fabric. In another example, cotton fibers tend to shrink significantly compared to synthetic fibers, even after several cycles of laundry. The shrinkage of cotton textile products, in particular clothing, poses a dilemma for consumers, because the consumers can not readily determine how much their newly purchased cotton clothing will shrink and if the clothing will fit on them to their satisfaction after a few cycles of wash. In yet another example, cotton fabrics tend to wrinkle easily, and require a great deal of care to maintain their shape.

[0004] In order to overcome these disadvantages, manufacturers often pre-treat cotton fibers and fabrics. For example, to control lint formation, cotton seeds are delinted prior to a brush delinter, or cotton fabrics are treated with a cellulase solution to remove lint precursors. To reduce wrinkle formation, manufacturers treat cotton fabrics with crosslinking agents, such as formaldehyde. However, these additional processes to treat cotton fibers or fabrics add cost to the manufacture of cotton textile products. Furthermore, chemicals added during the manufacture of cotton fabrics and fibers tend to wash out during laundering and lose their effect over time.

[0005] Thus, there is a need to improve the quality of cotton textile products. It would be desirable to avoid using any additives in improving the quality of cotton textile products, because they lose their effect over time, especially after repetitive laundering. Chemical additives may also be toxic to human body. It would also be desirable to reduce any additional processing steps so that the manufacture of cotton textile products will be cost effective. One way to resolve these problems is by improving the quality of cotton fibers themselves, so that the need for additional processing steps is eliminated. Thus, there is a need to improve the cotton fiber characteristics, such as fiber strength, fiber length and fineness.

SUMMARY OF THE INVENTION

[0006] The present invention provides isolated nucleic acid molecules comprising a FE polynucleotide sequences. Examples of nucleic acids of the invention include phosphoenol pyruvate carboxylase (PEPcase) sequences at least about 60% identical to SEQ ID NO:1, expansin sequences at least about 60% identical to SEQ ID NO:3, endoglucanase sequences at least about 60% identical to SEQ ID NO: 5, xyloglucan endoglycosyltransferse (XET) sequences at least about 60% identical to SEQ ID NO: 7, and pectin methyl esterase (PME) sequences at least about 60% identical to SEQ ID NO: 9. The isolated nucleic acid molecules of the invention may further comprise a plant promoter operably linked to the FE polynucleotide. The promoter may be, for example, a tissue-specific promoter, in particular, a fiber-specific promoter. The FE polynucleotides may be linked to the promoter in a sense or an antisense orientation.

[0007] The invention also provides transgenic plants comprising an expression cassette containing a plant promoter operably linked to a heterologous FE polynucleotide sequence of the invention.

[0008] The invention further provides methods of modulating fiber quality in a plant. The methods comprise introducing into the plant an expression cassette containing a plant promoter operably linked to a heterologous FE polynucleotide sequence of the invention. The plant may be any plant and is usually a member of the genus Gossypium. In the methods the expression cassette can be introduced into the plant through a sexual cross or using genetic engineering techniques.

DEFINITIONS

[0009] The phrase “nucleic acid sequence” refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5′ to the 3′ end. It includes chromosomal DNA, self-replicating plasmids, infectious polymers of DNA or RNA and DNA or RNA that performs a primarily structural role.

[0010] A “promoter” is defined as an array of nucleic acid control sequences that direct transcription of an operably linked nucleic acid. As used herein, a “plant promoter” is a promoter that functions in plants, even though obtained from other organisms, such as plant viruses. Promoters include necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. The term “operably linked” refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.

[0011] The term “plant” includes whole plants, plant organs (e.g., leaves, stems, flowers, roots, etc.), seeds and plant cells and progeny of same. The class of plants that can be used in the method of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), as well as gymnosperms. It includes plants of a variety of ploidy levels, including polyploid, diploid, haploid and hemizygous.

[0012] A polynucleotide sequence is “heterologous to” an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, a promoter operably linked to a heterologous coding sequence refers to a coding sequence from a species different from that from which the promoter was derived, or, if from the same species, a coding sequence which is different from any naturally occurring allelic variants.

[0013] A polynucleotide “exogenous to” an individual plant is a polynucleotide which is introduced into the plant by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation, biolistic methods, electroporation, and the like. Such a plant containing the exogenous nucleic acid is referred to here as an R₁ generation transgenic plant. Transgenic plants that arise from sexual cross or by selfing are descendants of such a plant.

[0014] “FE” is an acronym for fiber expansion, and the term is used generically to refer to properties of cotton fibers controlled by the polynucleotides and polypeptides of the present invention. For example, an FE polynucleotide refers to nucleic acids encoding FE polypeptides, such as phosphoenol pyruvate carboxylase (PEPcase), expansin, endoglucanase, xyloglucan endoglycosyltransferse (XET), and pectin methyl esterase (PME).

[0015] “Phosphoenol pyruvate carboxylase” or “PEPcase” refers to an enzyme that regulates synthesis of malate. Malate is a primary osmoregulatory solute involved in maintaining cell turgor during fiber expansion. Thus, a “phosphoenol pyruvate carboxylase polynucleotide” or “PEPcase polynucleotide” of the invention is a subsequence or full length polynucleotide sequence of a gene which, when present in a transgenic plant, can be used to modify fiber quality (e.g., fiber length, fiber strength, or fiber fineness) and which is at least about 60%, 70%, 80%, 90% or more identical to SEQ ID NO: 1. A PEPcase polynucleotide typically comprises or consists of a coding region of at least about 30-40 nucleotides to about 3400 nucleotides in length. Usually, the nucleic acids are from about 100 to about 500 nucleotides, often from about 500 to about 1500 nucleotides in length or from about 1500 nucleotides in length to about 3400 nucleotides in length.

[0016] “Expansin” refers to an enzyme that influences cross-linking relationships in the cell wall and allow cell wall components to “slip” during fiber expansion, thereby allowing the fibers to increase in length. Thus, an “expansin polynucleotide” of the invention is a subsequence or full length polynucleotide sequence of a gene which, when present in a transgenic plant, can be used to modify fiber quality (e.g., fiber length, fiber strength, or fiber fineness) and which is at least about 60%, 70%, 80%, 90% or more identical to SEQ ID NO:3. An expansin polynucleotide typically comprises or consists of a coding region of at least about 30-40 nucleotides to about 1154 nucleotides in length. Usually, the nucleic acids are from about 100 to about 500 nucleotides, often from about 500 to about 1154 nucleotides in length.

[0017] “Endoglucanase” refers to a type of cellulase that cleaves glucan cellulose, thereby controlling the length of cellulose polymers. Thus, an “endoglucanase polynucleotide” of the invention is a subsequence or full length polynucleotide sequence of a gene which, when present in a transgenic plant, can be used to modify fiber quality (e.g., fiber length, fiber strength, or fiber fineness) and which is at least about 60%, 70%, 80%, 90% or more identical to SEQ ID NO:5. An endoglucanase polynucleotide typically comprises or consists of a coding region of at least about 30-40 nucleotides to about 2386 nucleotides in length. Usually, the nucleic acids are from about 100 to about 500 nucleotides, often from about 500 to abou 1500 nucleotides in length or from about 1500 nucleotides in length to about 2386 nucleotides in length.

[0018] “Xyloglucan endoglycosyltranferase” or “XET” refers to an enzyme that modifies cross-linking relationships between cellulose microfibrils and the xyloglucan matrix, and loosens the cell wall. Thus, a “xyloglucan endoglycosyltransferase” or “XET” of the invention is a subsequence or full length polynucleotide sequence of a gene which, when present in a transgenic plant, can be used to modify fiber quality (e.g., fiber length, fiber strength, or fiber fineness) and which is at least about 60%, 70%, 80%, 90% or more identical to SEQ ID NO:7. A XET polynucleotide typically comprises or consists of a coding region of at least about 30-40 nucleotides to about 1179 nucleotides in length. Usually, the nucleic acids are from about 100 to about 500 nucleotides, often from about 500 to about 1179 nucleotides in length.

[0019] “Pectin methyl esterase” or “PME” refers to an enzyme that is involved in esterification of the pectin matrix. Thus, a “pectin methyl esterase” or “PME” of the invention is a subsequence or full length polynucleotide sequence of a gene which, when present in a transgenic plant, can be used to modify fiber quality (e.g., fiber length, fiber strength, or fiber fineness) and which is at least about 60%, 70%, 80%, 90% or more identical to SEQ ID NO:9. A PME polynucleotide typically comprises or consists of a coding region of at least about 30-40 nucleotides to about 1702 nucleotides in length. Usually, the nucleic acids are from about 100 to about 500 nucleotides, often from about 500 to about 1702 nucleotides in length.

[0020] For any polypeptides described above, one of skill in the art will recognize that in light of the present disclosure, various modifications (e.g., substitutions, additions, and deletions) can be made to the polypeptide sequences without substantially affecting their function. These variations are within the scope of the present invention.

[0021] In the case of both expression of transgenes and inhibition of endogenous genes (e.g., by antisense, or sense suppression) one of skill will recognize that the inserted polynucleotide sequence need not be “identical,” but may be only “substantially identical” to a sequence of the gene from which it was derived.

[0022] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.

[0023] The phrase “substantially identical,” in the context of two nucleic acids or polypeptides, refers to two or more sequences or subsequences that have at least about 60%, or at least about 70%, preferably at least about 80%, most preferably at least about 90-95% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. Preferably, the substantial identity exists over a region of the sequences that is at least about 50 residues in length, more preferably over a region of at least about 100 residues, and most preferably the sequences are substantially identical over at least about 150 residues. In a most preferred embodiment, the sequences are substantially identical over the entire length of the coding regions.

[0024] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

[0025] Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).

[0026] Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschuel et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).

[0027] In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

[0028] A further indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions, as described below.

[0029] “Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0030] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art.

[0031] The following six groups each contain amino acids that are conservative substitutions for one another:

[0032] 1) Alanine (A), Serine (S), Threonine (T);

[0033] 2) Aspartic acid (D), Glutamic acid (E);

[0034] 3) Asparagine (N), Glutamine (Q);

[0035] 4) Arginine (R), Lysine (K);

[0036] 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and

[0037] 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). (see, e.g., Creighton, Proteins (1984)).

[0038] An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below.

[0039] The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

[0040] The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, highly stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength pH. Low stringency conditions are generally selected to be about 15-30° C. below the T_(m). The T_(m) is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_(m), 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 time background hybridization.

[0041] Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cased, the nucleic acids typically hybridize under moderately stringent hybridization conditions.

[0042] In the present invention, genomic DNA or cDNA comprising nucleic acids of the invention can be identified in standard Southern blots under stringent conditions using the nucleic acid sequences disclosed here. For the purposes of this disclosure, suitable stringent conditions for such hybridizations are those which include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and at least one wash in 0.2×SSC at a temperature of at least about 50° C., usually about 55° C. to about 60° C., for 20 minutes, or equivalent conditions. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.

[0043] A further indication that two polynucleotides are substantially identical is if the reference sequence, amplified by a pair of oligonucleotide primers, can then be used as a probe under stringent hybridization conditions to isolate the test sequence from a cDNA or genomic library, or to identify the test sequence in, e.g., a northern or Southern blot.

[0044] “Fiber specific” promoter refers to promoters that preferentially promote gene expression in fiber cells over other cell types.

DETAILED DESCRIPTION

[0045] This invention provides plant FE genes that encode FE polypeptides, such as phosphoenol pyruvate carboxylase (PEPcase), expansin, endoglucanase, xyloglucan endoglycosyltransferase (XET), and pectin methyl esterase (PME). The invention further provides fiber-specific promoters. Still further, the invention provides molecular strategies for modulating fiber quality in fiber producing plants by modulating expression of FE genes or mutant forms of FE genes.

[0046] Important fiber properties, such as fiber length, strength, and fineness, are determined by rate and duration of fiber expansion. Fiber expansion is, in turn, dependent primarily on cell turgor, the driving force of fiber expansion, and the extensibility of the cell wall. By manipulating genes that regulate these critical processes, fiber growth and fiber properties can be modified.

[0047] There are several genes encoding enzymes that are involved in maintaining turgor during fiber expansion. One such enzyme is phosphoenol pyruvate carboxylase (PEPcase). A PEPcase regulates synthesis of malate, which is a primary osmoregulatory solute involved in maintaining cell turgor during fiber expansion. By modulating the expression of PEPcase, the rate and/or duration of fiber expansion and fiber length can be regulated.

[0048] There are also several enzymes that regulate extensibility of fiber cell walls. These include: 1) expansins; 2) endoglucanases; 3) xyloglucan endoglycosyltransferases (XET); and 4) pectin methyl esterases (PME).

[0049] Expansins influence cross-linking relationships in the cell wall and allow cell wall components to “slip” during fiber expansion, thereby allowing the fibers to increase in length.

[0050] Other enzymes are involved in cell wall relaxation during fiber expansion. For example, an endoglucanase is a cellulase that cleaves glucan cellulose, thereby controlling the length of cellulose polymers. Changing the cellulose polymer length in primary cell walls of developing fibers can strongly influence fiber length. In another example, XETs are important in cell wall loosening, by changing cross-linking relationships between cellulose microfibrils and the xyloglucan matrix. In yet another example, PMEs are enzymes that are involved in esterification of the pectin matrix. The pectin matrix is highly esterified during rapid fiber expansion. When esterified pectin fraction is deesterified, it results in increased cell wall rigidity during the termination of fiber expansion. Not wishing to be bound by a theory, delaying the deesterification of this pectin fraction can increase the duration of fiber expansion, and hence, fiber length.

[0051] A single FE or any combinations of the FE nucleic acids encoding the above enzymes can be introduced into a plant to modulate the quality of fibers. Preferably, a fiber-specific promoter is used to express the FE nucleic acids only in fibers of plants. More preferably, an inducible fiber specific promoter is used to express these genes during appropriate developmental stages most likely to result in increased fiber growth.

[0052] Isolation of Nucleic Acids

[0053] Generally, the nomenclature and the laboratory procedures in recombinant DNA technology described below are those well known and commonly employed in the art. Standard techniques are used for cloning, DNA and RNA isolation, amplification and purification. Generally enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like are performed according to the manufacturer's specifications. These techniques and various other techniques are generally performed according to Sambrook et al., Molecular Cloning—A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1989) or Current Protocols in Molecular Biology Volumes 1-3, John Wiley & Sons, Inc. (1994-1998).

[0054] The isolation of nucleic acids may be accomplished by a number of techniques. For instance, oligonucleotide probes based on the sequences disclosed here can be used to identify the desired gene in a cDNA or genomic DNA library. To construct genomic libraries, large segments of genomic DNA are generated by random fragmentation, e.g. using restriction endonucleases, and are ligated with vector DNA to form concatemers that can be packaged into the appropriate vector. To prepare a cDNA library, mRNA is isolated from the desired organ, such as leaves, and a cDNA library which contains gene transcripts is prepared from the mRNA. Alternatively, cDNA may be prepared from mRNA extracted from other tissues in which genes of interest or their homologs are expressed.

[0055] The cDNA or genomic library can then be screened using a probe based upon the sequence of a cloned gene disclosed here. Probes may be used to hybridize with genomic DNA or cDNA sequences to isolate homologous genes in the same or different plant species. Alternatively, antibodies raised against a polypeptide of interest can be used to screen an mRNA expression library.

[0056] Alternatively, the nucleic acids of interest can be amplified from nucleic acid samples using amplification techniques. For instance, polymerase chain reaction (PCR) technology can be used to amplify the sequences of genes directly from genomic DNA, from cDNA, from genomic libraries or cDNA libraries. PCR and other in vitro amplification methods may also be useful, for example, to clone nucleic acid sequences that code for proteins to be expressed, to make nucleic acids to use as probes for detecting the presence of the desired mRNA in samples, for nucleic acid sequencing, or for other purposes. For a general overview of PCR, see PCR Protocols: A Guide to Methods and Applications. (Innis, M, Gelfand, D., Sninsky, J. and White, T., eds.), Academic Press, San Diego (1990). Appropriate primers and probes for identifying sequences from plant tissues are generated from comparisons of the sequences provided herein (e.g. SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, etc.).

[0057] Polynucleotides may also be synthesized by well-known techniques, as described in the technical literature. See, e.g., Carruthers et al., Cold Spring Harbor Symp. Quant. Biol. 47:411-418 (1982), and Adams et al., J. Am. Chem. Soc. 105:661 (1983). Double stranded DNA fragments may then be obtained either by synthesizing the complementary strand and annealing the strands together under appropriate conditions, or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.

[0058] Increasing Levels of Gene Expression in Plant Fibers

[0059] The isolated nucleic acid sequences prepared as described herein can be used in a number of techniques. For example, the isolated nucleic acids can be introduced into plants to enhance endogenous gene expression. A particularly useful gene for this purpose is the FE genes shown in SEQ ID NO: 1, 3, 5, 7, and 9. In one embodiment, more than one gene can be introduced into plants. For example, expansins and endoglucanases can be expressed in plant fibers, thereby modifying crosslinking relationships and the cellulose polymer length in primary cell walls. Preferably, fiber tissues are targeted to increase expression FE genes. Fibers can be targeted at all times during the life of the plant e.g., using a constitutive promoter, or transiently, e.g., using a transiently active or an inducible promoter.

[0060] Isolated nucleic acids prepared as described herein can be used to introduce expression of particular FE nucleic acids to enhance endogenous gene expression. Enhanced expression will lead to increased fiber quality, such as fiber length, strength, and fineness. Thus, plants comprising these constructs are particularly useful for producing fibers with improved properties for textile products. Where overexpression of a gene is desired, the desired gene from a different species may be used to decrease potential sense suppression effects. One of skill will recognize that the polypeptides encoded by the genes of the invention, like other proteins, have different domains which perform different functions. Thus, the gene sequences need not be full length, as long as the desired functional domain of the protein is expressed.

[0061] Modified protein chains can also be readily designed utilizing various recombinant DNA techniques well known to those skilled in the art and described in detail below. For example, the chains can vary from the naturally occurring sequence at the primary structure level by amino acid substitutions, additions, deletions, and the like. These modifications can be used in a number of combinations to produce the final modified protein chain.

[0062] In another embodiment, modified forms of genes disclosed here can be used that have increased activity in vivo. For example, endoglucanase mutants that elongate the cellulose polymer length can be created and used to produce transgenic plants. Additional hyperactive forms can be readily identified, e.g., by screening for modified forms of FE enzymes with an increased ability to modify fiber quality such as fiber length, strength, and fineness.

[0063] In another embodiment, endogenous gene expression can be targeted for modification. Methods for introducing genetic mutations into plant genes and selecting plants with desired traits are well known. For instance, seeds or other plant material can be treated with a mutagenic chemical substance, according to standard techniques. Such chemical substances include, but are not limited to, the following: diethyl sulfate, ethylene imine, ethyl methanesulfonate and N-nitroso-N-ethylurea. Alternatively, ionizing radiation from sources such as X-rays or gamma rays can be used.

[0064] Alternatively, homologous recombination can be used to induce targeted gene modifications by specifically targeting the FE gene in vivo (see, generally, Grewal and Klar, Genetics 146: 1221-1238 (1997) and Xu et al., Genes Dev. 10: 2411-2422 (1996)). Homologous recombination has been demonstrated in plants (Puchta et al., Experientia 50: 277-284 (1994), Swoboda et al., EMBO J. 13: 484-489 (1994); Offringa et al., Proc. Natl. Acad. Sci. USA 90: 7346-7350 (1993); and Kempin et al., Nature 389:802-803 (1997)).

[0065] In applying homologous recombination technology to the genes of the invention, mutations in selected portions of a FE gene sequence (including 5′ upstream, 3′ downstream, and intragenic regions) such as those disclosed herein are made in vitro and then introduced into the desired plant using standard techniques. Since the efficiency of homologous recombination is known to be dependent on the vectors used, use of dicistronic gene targeting vectors as described by Mountford et al., Proc. Natl. Acad. Sci. USA 91: 4303-4307 (1994); and Vaulont et al., Transgenic Res. 4: 247-255 (1995) are conveniently used to increase the efficiency of selecting for altered FE expression in transgenic plants. The mutated gene will interact with the target wild-type gene in such a way that homologous recombination and targeted replacement of the wild-type gene will occur in transgenic plant cells, resulting in increased FE activity.

[0066] Alternatively, oligonucleotides composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends can be used. The RNA/DNA sequence is designed to align with the sequence of the target gene and to contain the desired nucleotide change. Introduction of the chimeric oligonucleotide on an extrachromosomal T-DNA plasmid results in efficient and specific FE gene conversion directed by chimeric molecules in a small number of transformed plant cells. This method is described in Cole-Strauss et al., Science 273:1386-1389 (1996) and Yoon et al., Proc. Natl. Acad. Sci. USA 93: 2071-2076 (1996).

[0067] One method to increase activity of desired gene products is to use “activation mutagenesis” (see, e.g., Hiyashi et al. Science 258:1350-1353 (1992)). In this method an endogenous gene can be modified to be expressed constitutively, ectopically, or excessively by insertion of T-DNA sequences that contain strong/constitutive promoters upstream of the endogenous gene. Activation mutagenesis of the endogenous gene will give the same effect as overexpression of the transgenic nucleic acid in transgenic plants. Alternatively, an endogenous gene encoding an enhancer of gene product activity or expression of the gene can be modified to be expressed by insertion of T-DNA sequences in a similar manner and FE activity can be increased.

[0068] Another strategy to increase gene expression can involve the use of dominant hyperactive mutants of the gene by expressing modified transgenes. For example, expression of a modified FE with a defective domain that is important for interaction with a negative regulator of FE activity can be used to generate dominant hyperactive FE proteins. Alternatively, expression of truncated FE which have only a domain that interacts with a negative regulator can titrate the negative regulator and thereby increase endogenous FE activity. Use of dominant mutants to hyperactivate target genes is described, e.g., in Mizukami et al., Plant Cell 8:831-845 (1996).

[0069] Suppression of FE Expression

[0070] A number of methods can be used to inhibit gene expression in plants. For instance, antisense technology can be conveniently used. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the antisense strand of RNA will be transcribed. The expression cassette is then transformed into plants and the antisense strand of RNA is produced. In plant cells, it has been suggested that antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy et al., Proc. Nat. Acad. Sci. USA, 85:8805-8809 (1988), and Hiatt et al., U.S. Pat. No. 4,801,340.

[0071] The nucleic acid segment to be introduced generally will be substantially identical to at least a portion of the endogenous embryo-specific gene or genes to be repressed. The sequence, however, need not be perfectly identical to inhibit expression. The vectors of the present invention can be designed such that the inhibitory effect applies to other proteins within a family of genes exhibiting homology or substantial homology to the target gene.

[0072] For antisense suppression, the introduced sequence also need not be full length relative to either the primary transcription product or fully processed mRNA. Generally, higher homology can be used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments may be equally effective. Normally, a sequence of between about 30 or 40 nucleotides and about full length nucleotides should be used, though a sequence of at least about 100 nucleotides is preferred, a sequence of at least about 200 nucleotides is more preferred, and a sequence of at least about 500 nucleotides is especially preferred.

[0073] Catalytic RNA molecules or ribozymes can also be used to inhibit expression of embryo-specific genes. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs.

[0074] Another method of suppression is sense suppression. Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter has been shown to be an effective means by which to block the transcription of target genes. For an example of the use of this method to modulate expression of endogenous genes see, Napoli et al., The Plant Cell 2:279-289 (1990), and U.S. Pat. Nos. 5,034,323, 5,231,020, and 5,283,184.

[0075] Generally, where inhibition of expression is desired, some transcription of the introduced sequence occurs. The effect may occur where the introduced sequence contains no coding sequence per se, but only intron or untranslated sequences homologous to sequences present in the primary transcript of the endogenous sequence. The introduced sequence generally will be substantially identical to the endogenous sequence intended to be repressed. This minimal identity will typically be greater than about 65%, but a higher identity might exert a more effective repression of expression of the endogenous sequences. Substantially greater identity of more than about 80% is preferred, though about 95% to absolute identity would be most preferred. As with antisense regulation, the effect should apply to any other proteins within a similar family of genes exhibiting homology or substantial homology.

[0076] For sense suppression, the introduced sequence in the expression cassette, needing less than absolute identity, also need not be full length, relative to either the primary transcription product or fully processed mRNA. This may be preferred to avoid concurrent production of some plants which are overexpressers. A higher identity in a shorter than full length sequence compensates for a longer, less identical sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and identity of non-coding segments will be equally effective. Normally, a sequence of the size ranges noted above for antisense regulation is used.

[0077] Preparation of Recombinant Vectors

[0078] To use isolated sequences in the above techniques, recombinant DNA vectors suitable for transformation of plant cells are prepared. Techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, for example, Weising et al., Ann. Rev. Genet. 22:421-477 (1988). A DNA sequence coding for the desired polypeptide, for example a cDNA sequence encoding a full length protein, will preferably be combined with transcriptional and translational initiation regulatory sequences which will direct the transcription of the sequence from the gene in the intended tissues of the transformed plant.

[0079] For example, for overexpression, a plant promoter fragment may be employed which will direct expression of the gene in all tissues of a regenerated plant. Such promoters are referred to herein as “constitutive” promoters and are active under most environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S and 19S transcription initiation regions; the full-length FMV transcript promoter (Gowda et al., J Cell Biochem 13D:301; the 1′- or 2′- promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes known to those of skill. Such promoters and others are described, e.g. in U.S. Pat. No. 5,880,330. Such genes include for example, ACT11 from Arabidopsis (Huang et al., Plant Mol. Biol. 33:125-139 (1996)), Cat3 from Arabidopsis (GenBank No. U43147, Zhong et al., Mol. Gen. Genet. 251:196-203 (1996)), the gene encoding stearoyl-acyl carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe et al. Plant Physiol. 104:1167-1176 (1994)), GPc1 from maize (GenBank No. X15596, Martinez et al. J. Mol. Biol 208:551-565 (1989)), and Gpc2 from maize (GenBank No. U45855, Manjunath et al., Plant Mol. Biol. 33:97-112 (1997)).

[0080] Alternatively, the plant promoter may direct expression of a nucleic acid in a specific tissue, organ or cell type (i.e., tissue-specific promoters) or may be otherwise under more precise environmental or developmental control (i.e., inducible promoters). Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, elevated temperature, the presence of light, or sprayed with chemicals/hormones. Numerous inducible promoters are known in the art, any of which can be used in the present invention. Such promoters include the yeast metallothionine promoter, which is activated by copper ions (see, e.g., Mett et al (1993) PNAS 90:4567), the dexamethasone-responsive promoter, In2-1 and In2-2, which are activated by substituted benzenesulfonamides, and GRE regulatory sequences, which are glucocorticoid-responsive (Schena et al., Proc. Natl. Acad. Sci. U.S.A. 88: 0421 (1991)).

[0081] Tissue-specific promoters can be inducible. Similarly, tissue-specific promoters may only promote transcription within a certain time frame of developmental stage within that tissue. Other tissue specific promoters may be active throughout the life cycle of a particular tissue. One of skill will recognize that a tissue-specific promoter may drive expression of operably linked sequences in tissues other than the target tissue. Thus, as used herein a tissue-specific promoter is one that drives expression preferentially in the target tissue or cell type, but may also lead to some expression in other tissues as well.

[0082] In preferred embodiments, promoters that drive fiber-specific expression of polynucleotides can be used. Such expression can be achieved under the control of the fiber-specific promoters described, for example, in U.S. Pat. No. 5,495,070. Typically, the nucleic acids of the invention are operably linked to a promoter active primarily during the stages of cotton fiber cell elongation, e.g., as described by Rinehart (1996) Plant Physiol. 112:1131-1141. See also, John (1997) Proc. Natl. Acad. Sci. USA 89:5769-5773; John, et al., U.S. Pat. Nos. 5,608,148 and 5,602,321, describing cotton fiber-specific promoters and methods for the construction of transgenic cotton plants.

[0083] Additional promoters which are linked to genes found to be expressed preferentially in cotton fiber cells can also be identified and isolated for incorporation into the expression cassettes and vectors of the invention. They care also used to express ABP nucleic acids in a cotton fiber specific (or fiber-preferential) manner. As the coding sequences for these tissue specific genes have been characterized, identification and isolation of these cotton fiber specific promoters can be accomplished using standard genetic engineering techniques. For example, Shimizu (1997) Plant Cell Physiol. 38:375-378, found that both endo-1,4-beta-glucanase and expansin mRNA levels were high during cotton fiber cell elongation, but decreased when cell elongation ceased. Xyloglucan also decreased. The endo-1,3-beta-glucanase mRNA level was very low in the elongating cells, but increased gradually at the onset of secondary wall synthesis, accompanying the massive deposition of cellulose. Also, as discussed above, Song (1997) supra, found a cotton fiber-specific acyl-carrier protein in Gossypium hirsutum. Ma (1997) Biochim. Biophys. Acta 1344:111-114, found a cotton fiber-specific cDNA encoding a lipid transfer protein. See also John, U.S. Pat. No. 5,597,718, describing means to identify cotton fiber-specific genes by differential cDNA library screenings.

[0084] Root-specific promoters may also be used in some embodiments of the present invention. Examples of root-specific promoters include the promoter from the alcohol dehydrogenase gene (DeLisle et al. Int. Rev. Cytol. 123, 39-60 (1990)).

[0085] Further examples include, e.g., ovule-specific, embryo-specific, endosperm-specific, integument-specific, seed coat-specific, or some combination thereof. A leaf-specific promoter has been identified in maize, Busk (1997) Plant J. 11:1285-1295. The ORF13 promoter from Agrobacterium rhizogenes exhibits high activity in roots (Hansen (1997) supra). A maize pollen-specific promoter has been identified, Guerrero (1990) Mol. Gen. Genet. 224:161-168). A tomato promoter active during fruit ripening, senescence and abscission of leaves and, to a lesser extent, of flowers can be used (Blume (1997) Plant J. 12:731-746); or a pistil-specific promoter from the potato SK2 gene, encoding a pistil-specific basic endochitinase (Ficker (1997) Plant Mol. Biol. 35:425-431). The Blec4 gene from pea is active in epidermal tissue of vegetative and floral shoot apices of transgenic alfalfa, making it a useful tool to target the expression of foreign genes to the epidermal layer of actively growing shoots or fibers. Another tissue-specific plant promoter is the ovule-specific BEL1 gene (Reiser (1995) Cell 83:735-742, GenBank No. U39944). See also Klee, U.S. Pat. No. 5,589,583, describing a plant promoter region is capable of conferring high levels of transcription in meristematic tissue and/or rapidly dividing cells.

[0086] One of skill will recognize that a tissue-specific promoter may drive expression of operably linked sequences in tissues other than the target tissue. Thus, as used herein a tissue-specific promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other tissues as well.

[0087] If proper polypeptide expression is desired, a polyadenylation region at the 3′-end of the coding region should be included. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA.

[0088] The vector comprising the sequences (e.g., promoters or coding regions) from genes of the invention will typically comprise a marker gene that confers a selectable phenotype on plant cells. For example, the marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or Basta.

[0089] Production of Transgenic Plants

[0090] DNA constructs of the invention may be introduced into the genome of the desired plant host by a variety of conventional techniques. For example, the DNA construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the DNA constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment.

[0091] Microinjection techniques are known in the art and well described in the scientific and patent literature. The introduction of DNA constructs using polyethylene glycol precipitation is described in Paszkowski et al. Embo. J. 3:2717-2722 (1984). Electroporation techniques are described in Fromm et al. Proc. Natl. Acad. Sci. USA 82:5824 (1985). Ballistic transformation techniques are described in Klein et al. Nature 327:70-73 (1987).

[0092] Alternatively, the DNA constructs may be combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector. The virulence functions of the Agrobacterium tumefaciens host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria. Agrobacterium tumefaciens-mediated transformation techniques, including disarming and use of binary vectors, are well described in the scientific literature. See, for example Horsch et al., Science 233:496-498 (1984), and Fraley et al. Proc. Natl. Acad. Sci. USA 80:4803 (1983) and Gene Transfer to Plants, Potrykus, ed. (Springer-Verlag, Berlin 1995).

[0093] Transformed plant cells which are derived by any of the above transformation techniques can be cultured to regenerate a whole plant which possesses the transformed genotype and thus the desired phenotype such as increased fiber length, strength or fineness. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee et al. Ann. Rev. of Plant Phys. 38:467-486 (1987).

[0094] The nucleic acids of the invention can be used to confer desired traits on essentially any fiber producing plants. These plants include cotton plants (Gossypium arboreum, Gossypium herbaceum, Gossypium barbadense and Gossypium hirsutum), silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfal, balsa, ramie, kenaf, hemp (Cannabis sativa), roselle, jute, sisal abaca and flax.

[0095] One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.

[0096] Using known procedures one of skill can screen for plants of the invention by detecting the increase or decrease of an mRNA or protein of interest in transgenic plants. Means for detecting and quantifying mRNAs or proteins are well known in the art.

[0097] Assessing Fiber Quality

[0098] Fibers produced from the transgenic plants transformed with FE nucleic acids are compared to control fibers (e.g., fibers from native plants or plants transformed with marker nucleic acids) to determine the extent of modulation of fiber properties. Modulation of fiber properties, such as fiber length, strength, or fineness, is achieved when the percent difference in these fiber properties of transgenic plants and control plants is at least about 10%, preferably at least about 20%, most preferably at least about 30%.

[0099] Several parameters can be measured to compare the properties or quality of fibers produced from transgenic plants transformed with FE nucleic acids and the quality of fibers produced from native plants. These include: 1) fiber length; 2) fiber strength; and 3) fineness of fibers.

[0100] A number of methods are known in the art to measure these parameters. See, e.g., U.S. Pat. No. 5,495,070, incorporated herein by reference. For example, instruments such as a fibrograph and HVI (high volume instrumentation) systems can be used to measure the length of fibers. The HVI systems can also be used to measure fiber strength. Fiber strength generally refers to the force required to break a bundle of fibers or a single fiber. In HVI testing, the breaking force is expressed in terms of “grams force per tex unit.” This is the force required to break a bundle of fibers that is one tex unit in size. In addition, fineness of fibers can be measured, e.g., from a porous air flow test. In a porous air flow test, a weighed sample of fibers is compressed to a given volume and controlled air flow is passed through the sample. The resistance to the air flow is read as micronaire units. The micronaire readings reflect a combination of maturity and fineness. Using these and other methods known in the art, one of skill can readily determine the extent of modulation of fiber characteristics or quality in transgenic plants.

EXAMPLES

[0101] The following examples are offered to illustrate, but not to limit the claimed invention.

Example 1

[0102] A full-length cDNA encoding a fiber-PEPC was isolated from a cotton fiber cDNA library. The characteristic features of the complete cDNA clone, designated PEPC1, are described below. PEPC1 gene expression in cotton was evaluated by RT-PCR using total RNA and clone specific primers (Table 1). PEPC1 was expressed in fibers, embryos, and roots, but not in the light-exposed tissues of leaves, bracts, petals, or stigma. The expression of PEPC1 was higher in fibers collected between 10 to 15 days post anthesis (DPA) when compared to the ovule, embryo and root tissues.

[0103] Developmental changes of PEPC1 expression in fiber (5 to 25 DPA) paralleled the rate of fiber elongation and peaked around the day of maximum cell expansion. Cotton PEPC1 showed a higher level of amino acid identity to the C3-type enzyme from plant species (86-89% identity and 5-7% similarity) compared to 76-86% identity to the C4-type enzyme. These observations suggest that the PEPC1 gene is tissue-specific and can be categorized as a C3-dark PEPC isoform.

[0104] The partial cotton PEPC cDNA clone of 577 bp encodes the C-terminal portion of the enzyme. Sequence comparison of PEPC1 and PEPC2 cDNAs showed 80% nucleotide identity, and the deduced amino acid sequences revealed 87% amino acid identity and 6.3% similarity. Overlapping sequence information confirmed that PEPC2 represents a second highly homologous PEPC gene expressed in developing cotton fibers (Gossypium hirsufum L.).

[0105] Cloning Techniques:

[0106] A λunizap II cDNA library, constructed from developing cotton fibers (10 days post-anthesis), was screened with a 577 by PCR product as a homologous hybridization probe. The PEPC2 cDNA probe was prepared by PCR-amplification with the primer-set, COT189 (5=-CCATGGATCTTTGCCTGGAC-3=) and COT185 (5=-GCATTCCAGCAGCAATACC-3=), which were designed to conserved regions of PEPC in other plant organisms. The partial cDNA was cloned into pCRII. Both strands of the partial cDNA and the full-length cDNA in pBluescript SK (−) were sequenced by the dideoxy-chain termination method using vector-specific and synthetic oligonucleotide primers.

[0107] Comparison of the nucleotide and the deduced amino acid sequences to alfalfa (AC M83086), Flaveria australasica (AC Z25853), Flaveria pringlef (AC X64144), Flaveria trinervia (AC X64143), maize (AC X61489), potato (AC X67053), rape seed (AC D13987), sorghum (AC X65137), sorghum (AC X59925), soybean (AC D10717), and tobacco (AC X59016) homologs.

[0108] The PEPC1 cDNA is 3405 bp in length, containing 288 bp 5=-UTR, 2898 bp coding region, and 219 by 3=-UTR. Translation start and stop codons are positioned at nucleotides 289 and 3184, respectively. 44.7% (G+C) content in protein coding region.

[0109] The 2898-by open reading frame of PEPC1 encodes a polypeptide of 965 amino acids with a predicted Mr of 110,183, an isoelectric point of 5.95, and an aliphatic index of 88.54. The total numbers of negatively charged (ASP+GLU) and positively charged (ARG+LYS) residues are 143 and 127, respectively. There is a conserved phosphorylation site at residue 11 (Ser). His-172 and Lys-600, which are essential for enzyme activity, are located in conserved motifs (Chollet et al., 1996). The deduced amino acid sequence exhibits a 79-89% identity and a 5.3-6.9% similarity to the PEPC of other plants.

[0110] Protein Homology:

[0111] Alignment of PEPC amino acids (data not shown) reveals some highly conserved regions between these enzymes, which are distributed along the protein. A glycine-rich motif, FHGRGGXXGRGG, found in all PEPC enzymes, is proposed to be involved in the binding of PEP (Iterada et al., 1992). Another highly conserved sequence, GYSDSXKDXG, contains the lysine residue implicated in the activity of PEPC (Jiao et al., 1990). The VXTAHPT motif (amino acid 168-174) contains a histidine residue, which has been suggested to be essential for activity (Chollet et al., 1996; Andreo et al., 1987). Furthermore, a sequence closely related to the phosphorylation site, E/DK/R-X-X-SIDAQLR (Jiao et al., 1990), which is conserved in C3 and C4 plants, is also found in the N-terminal region of the cotton PEPC. It is suggested that non photosynthetic PEPCs from C3 and C4 plants undergo regulatory phosphorylation similar to their C4 and CAM photosynthetic counterparts (Lepiniec et al., 1994).

[0112] Expression Characteristics:

[0113] The expression of PEPC in different tissues (fiber, embryo, root, leaf, bract, petal and stigma) was tested by quantitative RT-PCR using 500 ng total RNA and a set of clone-specific primers, COT 285 (5=-CTTTCTGCGGAGTACGAAG-3=) and COT 288 (5=-CCTGCTCTCATCTCATCTTG-3=). PEPC1 was expressed in fibers, embryos, and roots but not in the light-exposed tissues of leaves, bracts, petals, or stigma. The developmental expression of PEPC1 in fiber peaked around the day of maximum fiber elongation.

[0114] It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

1 23 1 3405 DNA Gossypium hirsutum phosphoenolpyruvate carboxylase 1 (PEPC1) (PEPcase) 1 tttcactttc tggtgttcag tcataagtta cccattattt tatctgtttt tctagcgatt 60 tcttggtgtg gggcatcacg gaattcactt ccaaagagat aggatttgat tcatcttttg 120 ttttccgggt ttgggtttgg gttcggcgga ttcttcgcca caaattattt ttatcctttt 180 acaccgcaaa ataataaatt tcatccgtaa ttgttccttt ctttttcctg cctttcattg 240 gttcataatt taaagttttg gctttggtag tcaagtaaaa agacagagat ggcaggtaga 300 aaagtagaga agatggcttc aatagatgca caactaaggc tattagcacc tgggaaagtc 360 tctgaggatg ataagttggt tgaatatgat gctgtgctac tggatcgttt tcttgatatt 420 cttcaggatt tgcatggaga ggatatcaga gaaacggttc aagaatgcta cgagctttct 480 gcggagtacg aaggaaagca tgatcctaaa atattggagg agcttggcaa ggtacttaca 540 agcttggatc ctggggactc aattgttgtt accaaatcat tttcccacat gcttaacttg 600 ggaaacttgg ccgaggaggt tcaaattgca tatagacgaa ggattaagtt gaagaaagga 660 gattttgctg atgagagttc agcaacaact gaatcagata ttgaagagac gttcaagcga 720 cttgtggggc agttgaacaa gtcccctgaa gaagtttttg atgctttgaa gaatcagact 780 gtagatttag tcttaactgc acatcctaca cagtctgttc gaagatcttt acttcaaaaa 840 cacggaagga tacgtaattg tttgacacaa ttgtatgcta aagacattac acctgatgat 900 aagcaggaac ttgatgaggc actacaaagg gagattcaag ctgcttttcg cacagatgag 960 atccgaagga atcctcccac cccacaagat gagatgagag caggaatgag ctacttccac 1020 gagacaatct ggaaaggtgt accaaaattc ttgcgtcgtg ttgacacagc tttgaagaac 1080 atagggataa atgaacgtgt tccatacaat gcccctctta ttcaattctc ttcatggatg 1140 ggaggggatc gtgatggaaa ccccagggta actcctgaag ttacaagaga tgtctgctta 1200 ttagctagaa tgatggctgc taacttgtac ttctcccaaa tagaggatct tatgtttgag 1260 ttatcaatgt ggcgttgcag cgatgaactt cgtattcgtg cagatgaact ccataggtcc 1320 tccaaaaagg atgcaaagca ttacatagaa ttttggaaac agattcctcc aaatgagcca 1380 tatcgcatta ttcttggtga tgtgagggac aagctgtata atacacgtga acgtgctcgt 1440 agcctgttgg ccaatggatt ttctgacatt cctgaagaag cagcatttac caatgtggag 1500 cagtttctgg agcctcttga actctgctat agatcactct gtgcttgtgg tgatcggcca 1560 atagctgatg gaagccttct tgatttctta cggcaagttt ctacctttgg gctttcactt 1620 gtgaggcttg atatccgaca ggaatctgat agacatactg atgtccttga tgctatcaca 1680 aagcacctgg atattggatc ttatcgagaa tggcctgagg aacgccgaca ggaatggctc 1740 ttatctgaac tcagaggcaa gcgccctcta ttcggccctg atcttcccaa aacagaagaa 1800 gtcgctgatg tattggacac atttcatgtc atttctgaac tgccttcaga cagctttggt 1860 gcctatataa tctcaatggc tacagcccca tctgatgtgc ttgctgttga gcttttacaa 1920 cgtgaatgcc atgtaaagca accattacgg gtagttccat tgtttgaaaa actcgctgat 1980 cttgaagctg ctcctgctgc tgtggctcgt ctcttctcta tagattggta cagagaccgg 2040 atcaatggga aacaggaagt gatgataggt tattcagatt caggaaagga tgctggccgt 2100 ctttctgcag catggcagct atacaaggct caggaggaac ttgtaaaggt ggcaaagcag 2160 tatggtgtta agcttacaat gttccatggc cgaggaggga cagttggaag aggaggggga 2220 cccacgcatc ttgctatatt gtctcaacca cccgatacaa ttcatggatc acttcgtgta 2280 acagttcaag gtgaagttat tgaacaatca tttggagagg agcacttgtg cttcaggacg 2340 cttcaacgtt ttactgctgc tacacttgag catggaatgc atccccctgt ctcaccaaat 2400 ccagaatggc gtgcactcat ggatgaaatg gcagtagttg caacaaagga ataccgttct 2460 gtagtcttcc aggaacctcg ctttgttgaa tacttccgcc tagcaacacc agaattggag 2520 tatggtcgga tgaatattgg aagccgtcca tcaaaaagga aaccaagtgg aggcattgaa 2580 tcactccgtg caatcccatg gatctttgca tggactcaaa caagatttca tttacctgtg 2640 tggcttggct ttggggctgc atttaagcac gtcattcaga aggatataaa gaatctccac 2700 atgctccagg agatgcacaa ccaatggcct ttctttaggg tcacaatgga cttaattgaa 2760 atggtatttg ccaagggaga ccctggaatc gctgccttat atgacaagct gctagtgtca 2820 aaggaactct ggccctttgg agagaacttg agagctaact atgaagacac taaacgactt 2880 gttctccagg ttgctggaca cagagatctt cttgaaggtg acccttacct gaagcagagg 2940 ctccgacttc gtgatgctta catcacaacc cttaatgtgt gccaagcgta cactttgaaa 3000 aggatccgtg accctgatta tcatgtcaag gtcaggcctc acttatccag ggaatacatg 3060 gaatcaagca aggcggcagc tgagcttgtg aaacttaacc ctacaagcga gtatgctcct 3120 ggtctggaag acacccttat tttgaccatg aagggtattg ctgctggaat gcaaaacact 3180 ggttaaaact tgcggattgt tgtttccttg tgttgttatg ctccttagtt tatttttaat 3240 ggatgttgct ttgcgtcaag taaacctttt atattactat tattatcggt tgggttaatt 3300 tcatatttgg ctcatatatt actaagtgtt gtcagtctgg tatctctata ataatacata 3360 ttaacatgat ttcccattca aaaaaaaaaa aaaaaaaaaa aaaaa 3405 2 965 PRT Gossypium hirsutum 2 Met Ala Gly Arg Lys Val Glu Lys Met Ala Ser Ile Asp Ala Gln Leu 1 5 10 15 Arg Leu Leu Ala Pro Gly Lys Val Ser Glu Asp Asp Lys Leu Val Glu 20 25 30 Tyr Asp Ala Val Leu Leu Asp Arg Phe Leu Asp Ile Leu Gln Asp Leu 35 40 45 His Gly Glu Asp Ile Arg Glu Thr Val Gln Glu Cys Tyr Glu Leu Ser 50 55 60 Ala Glu Tyr Glu Gly Lys His Asp Pro Lys Ile Leu Glu Glu Leu Gly 65 70 75 80 Lys Val Leu Thr Ser Leu Asp Pro Gly Asp Ser Ile Val Val Thr Lys 85 90 95 Ser Phe Ser His Met Leu Asn Leu Gly Asn Leu Ala Glu Glu Val Gln 100 105 110 Ile Ala Tyr Arg Arg Arg Ile Lys Leu Lys Lys Gly Asp Phe Ala Asp 115 120 125 Glu Ser Ser Ala Thr Thr Glu Ser Asp Ile Glu Glu Thr Phe Lys Arg 130 135 140 Leu Val Gly Gln Leu Asn Lys Ser Pro Glu Glu Val Phe Asp Ala Leu 145 150 155 160 Lys Asn Gln Thr Val Asp Leu Val Leu Thr Ala His Pro Thr Gln Ser 165 170 175 Val Arg Arg Ser Leu Leu Gln Lys His Gly Arg Ile Arg Asn Cys Leu 180 185 190 Thr Gln Leu Tyr Ala Lys Asp Ile Thr Pro Asp Asp Lys Gln Glu Leu 195 200 205 Asp Glu Ala Leu Gln Arg Glu Ile Gln Ala Ala Phe Arg Thr Asp Glu 210 215 220 Ile Arg Arg Asn Pro Pro Thr Pro Gln Asp Glu Met Arg Ala Gly Met 225 230 235 240 Ser Tyr Phe His Glu Thr Ile Trp Lys Gly Val Pro Lys Phe Leu Arg 245 250 255 Arg Val Asp Thr Ala Leu Lys Asn Ile Gly Ile Asn Glu Arg Val Pro 260 265 270 Tyr Asn Ala Pro Leu Ile Gln Phe Ser Ser Trp Met Gly Gly Asp Arg 275 280 285 Asp Gly Asn Pro Arg Val Thr Pro Glu Val Thr Arg Asp Val Cys Leu 290 295 300 Leu Ala Arg Met Met Ala Ala Asn Leu Tyr Phe Ser Gln Ile Glu Asp 305 310 315 320 Leu Met Phe Glu Leu Ser Met Trp Arg Cys Ser Asp Glu Leu Arg Ile 325 330 335 Arg Ala Asp Glu Leu His Arg Ser Ser Lys Lys Asp Ala Lys His Tyr 340 345 350 Ile Glu Phe Trp Lys Gln Ile Pro Pro Asn Glu Pro Tyr Arg Ile Ile 355 360 365 Leu Gly Asp Val Arg Asp Lys Leu Tyr Asn Thr Arg Glu Arg Ala Arg 370 375 380 Ser Leu Leu Ala Asn Gly Phe Ser Asp Ile Pro Glu Glu Ala Ala Phe 385 390 395 400 Thr Asn Val Glu Gln Phe Leu Glu Pro Leu Glu Leu Cys Tyr Arg Ser 405 410 415 Leu Cys Ala Cys Gly Asp Arg Pro Ile Ala Asp Gly Ser Leu Leu Asp 420 425 430 Phe Leu Arg Gln Val Ser Thr Phe Gly Leu Ser Leu Val Arg Leu Asp 435 440 445 Ile Arg Gln Glu Ser Asp Arg His Thr Asp Val Leu Asp Ala Ile Thr 450 455 460 Lys His Leu Asp Ile Gly Ser Tyr Arg Glu Trp Pro Glu Glu Arg Arg 465 470 475 480 Gln Glu Trp Leu Leu Ser Glu Leu Arg Gly Lys Arg Pro Leu Phe Gly 485 490 495 Pro Asp Leu Pro Lys Thr Glu Glu Val Ala Asp Val Leu Asp Thr Phe 500 505 510 His Val Ile Ser Glu Leu Pro Ser Asp Ser Phe Gly Ala Tyr Ile Ile 515 520 525 Ser Met Ala Thr Ala Pro Ser Asp Val Leu Ala Val Glu Leu Leu Gln 530 535 540 Arg Glu Cys His Val Lys Gln Pro Leu Arg Val Val Pro Leu Phe Glu 545 550 555 560 Lys Leu Ala Asp Leu Glu Ala Ala Pro Ala Ala Val Ala Arg Leu Phe 565 570 575 Ser Ile Asp Trp Tyr Arg Asp Arg Ile Asn Gly Lys Gln Glu Val Met 580 585 590 Ile Gly Tyr Ser Asp Ser Gly Lys Asp Ala Gly Arg Leu Ser Ala Ala 595 600 605 Trp Gln Leu Tyr Lys Ala Gln Glu Glu Leu Val Lys Val Ala Lys Gln 610 615 620 Tyr Gly Val Lys Leu Thr Met Phe His Gly Arg Gly Gly Thr Val Gly 625 630 635 640 Arg Gly Gly Gly Pro Thr His Leu Ala Ile Leu Ser Gln Pro Pro Asp 645 650 655 Thr Ile His Gly Ser Leu Arg Val Thr Val Gln Gly Glu Val Ile Glu 660 665 670 Gln Ser Phe Gly Glu Glu His Leu Cys Phe Arg Thr Leu Gln Arg Phe 675 680 685 Thr Ala Ala Thr Leu Glu His Gly Met His Pro Pro Val Ser Pro Asn 690 695 700 Pro Glu Trp Arg Ala Leu Met Asp Glu Met Ala Val Val Ala Thr Lys 705 710 715 720 Glu Tyr Arg Ser Val Val Phe Gln Glu Pro Arg Phe Val Glu Tyr Phe 725 730 735 Arg Leu Ala Thr Pro Glu Leu Glu Tyr Gly Arg Met Asn Ile Gly Ser 740 745 750 Arg Pro Ser Lys Arg Lys Pro Ser Gly Gly Ile Glu Ser Leu Arg Ala 755 760 765 Ile Pro Trp Ile Phe Ala Trp Thr Gln Thr Arg Phe His Leu Pro Val 770 775 780 Trp Leu Gly Phe Gly Ala Ala Phe Lys His Val Ile Gln Lys Asp Ile 785 790 795 800 Lys Asn Leu His Met Leu Gln Glu Met His Asn Gln Trp Pro Phe Phe 805 810 815 Arg Val Thr Met Asp Leu Ile Glu Met Val Phe Ala Lys Gly Asp Pro 820 825 830 Gly Ile Ala Ala Leu Tyr Asp Lys Leu Leu Val Ser Lys Glu Leu Trp 835 840 845 Pro Phe Gly Glu Asn Leu Arg Ala Asn Tyr Glu Asp Thr Lys Arg Leu 850 855 860 Val Leu Gln Val Ala Gly His Arg Asp Leu Leu Glu Gly Asp Pro Tyr 865 870 875 880 Leu Lys Gln Arg Leu Arg Leu Arg Asp Ala Tyr Ile Thr Thr Leu Asn 885 890 895 Val Cys Gln Ala Tyr Thr Leu Lys Arg Ile Arg Asp Pro Asp Tyr His 900 905 910 Val Lys Val Arg Pro His Leu Ser Arg Glu Tyr Met Glu Ser Ser Lys 915 920 925 Ala Ala Ala Glu Leu Val Lys Leu Asn Pro Thr Ser Glu Tyr Ala Pro 930 935 940 Gly Leu Glu Asp Thr Leu Ile Leu Thr Met Lys Gly Ile Ala Ala Gly 945 950 955 960 Met Gln Asn Thr Gly 965 3 1153 DNA Gossypium hirsutum expansin 3 ggcacgaggg tcagccaatt gtttgagcta gctagctctt actcaaatgg caaccaaaac 60 gatgatgttg caaatatttt cacttttctt ctttttgttc agtatctgca actccatttt 120 ccttggtgct aatggagatg acaatggtgg ttggcaaact gcccatgcca ccttctacgg 180 tggtgctgat gctaccggca caatgggggg agcttgtggt tatggaaacc tgtacagtca 240 agggtatgga acgagcacag cagctttgag cactgcactt ttcaacaatg gcttgagctg 300 cggtgccttc tacgagctcc ggtgcaacaa tgatcctcaa tggtgcatta gtcgaaccat 360 aaccgtgaca gccaccaact tttgtccccc taactatgct ttatctagtg acaatggcgg 420 gtggtgcaat cccccacgag aacactttga tttggccgaa ccggcattct tgcagatcgc 480 ggaatatcga gctgggatcg tccctgttat gttcagaagg gtgtcatgtg tgaagaaagg 540 aggcatcagg tacaccatga atggacattc gtacttcaac atggtgttga taaccaacgt 600 gggaggggca ggggatataa cgtcagtgtc catcaagggt tccaaaacag gatggctacc 660 tatgtccaga aattggggcc aaaactggca gagcaatgct taccttaacg gccaaagcct 720 ctctttcaaa gtgactgcca gcgatagcag gactatcaca aactacaatg tagtgcccgc 780 tggttggcaa ttcggacaaa cttttgaagg aggccagttt taagacaata ttatagtgtc 840 cgtctaatat taaaactgga attgacatat tacttatata aggcacatga gcgttttatg 900 ccgaggtagc aaagtggcgc ccgctggctt tatgtgtgaa ataggcgagc aagtgccatt 960 agcctataat atacacattt cctatagtga accaaactat taagtttgaa ctctagaagt 1020 gatatccata atgtctgaaa tttgattgtt gatgattgac catgatattt atggttttca 1080 ttattgaaat acttttttat tataatttat aaataaatga atcatttctt tttacaaaaa 1140 aaaaaaaaaa aaa 1153 4 258 PRT Gossypium hirsutum 4 Met Ala Thr Lys Thr Met Met Leu Gln Ile Phe Ser Leu Phe Phe Phe 1 5 10 15 Leu Phe Ser Ile Cys Asn Ser Ile Phe Leu Gly Ala Asn Gly Asp Asp 20 25 30 Asn Gly Gly Trp Gln Thr Ala His Ala Thr Phe Tyr Gly Gly Ala Asp 35 40 45 Ala Thr Gly Thr Met Gly Gly Ala Cys Gly Tyr Gly Asn Leu Tyr Ser 50 55 60 Gln Gly Tyr Gly Thr Ser Thr Ala Ala Leu Ser Thr Ala Leu Phe Asn 65 70 75 80 Asn Gly Leu Ser Cys Gly Ala Phe Tyr Glu Leu Arg Cys Asn Asn Asp 85 90 95 Pro Gln Trp Cys Ile Ser Arg Thr Ile Thr Val Thr Ala Thr Asn Phe 100 105 110 Cys Pro Pro Asn Tyr Ala Leu Ser Ser Asp Asn Gly Gly Trp Cys Asn 115 120 125 Pro Pro Arg Glu His Phe Asp Leu Ala Glu Pro Ala Phe Leu Gln Ile 130 135 140 Ala Glu Tyr Arg Ala Gly Ile Val Pro Val Met Phe Arg Arg Val Ser 145 150 155 160 Cys Val Lys Lys Gly Gly Ile Arg Tyr Thr Met Asn Gly His Ser Tyr 165 170 175 Phe Asn Met Val Leu Ile Thr Asn Val Gly Gly Ala Gly Asp Ile Thr 180 185 190 Ser Val Ser Ile Lys Gly Ser Lys Thr Gly Trp Leu Pro Met Ser Arg 195 200 205 Asn Trp Gly Gln Asn Trp Gln Ser Asn Ala Tyr Leu Asn Gly Gln Ser 210 215 220 Leu Ser Phe Lys Val Thr Ala Ser Asp Ser Arg Thr Ile Thr Asn Tyr 225 230 235 240 Asn Val Val Pro Ala Gly Trp Gln Phe Gly Gln Thr Phe Glu Gly Gly 245 250 255 Gln Phe 5 2386 DNA Gossypium hirsutum endo-1,4-beta-D-glucanase (EGase) 5 ggcacgagcc actttggaaa accaatgaag aaagcaccac tgcctactta tacacatttt 60 atttatcaaa ctcaacttcc tcttcgtctt ggtagatcag atctgtcggt gctcctgcat 120 tttccgccca ctactcttcc aaatcctcat catgtacggc agaaatccgt ggggaggtcc 180 cctggagata aacgccactg attctgccac tgacgacgac aggagcagga atctgcagga 240 cctggatagg gctgcactct ctcgcccctt ggacgagact cagcaaagct ggctgcttgg 300 ccccggggag caaaagaaga agaagaagta cgttgatctc ggatgtatca ttgtgagccg 360 caagatcttt gtatggaccg tggggaccct gctagtctcc gccctcctgg ccggactcat 420 caccctcatc gtcaagactg tcccacgtca tcaccaccgc cactctccgc ccgataacta 480 cactctggct cttcacaagg cgctcatgtt ctttaatgct cagcgttctg gaaagctgcc 540 caagcataat aatgtgtcgt ggagagggaa ctcgggcctc caagatggca aatccgatcc 600 ctccgttttg atgaaagatc tggtcggcgg atattacgat gctggagatg ctatcaagtt 660 taactttcct gcatcttttt caatgactat gttgagctgg agtgtcatcg aatacagtgc 720 taaatacgag gctgccggcg agctcaatca tgttaaagag atcatcaaat ggggtactga 780 ttatcttctg aagaccttca acaatactgc tgataccatt gacaggattg cagcgcaggt 840 agggatagga gatacatctg gaggagtttc agccccaaat gatcattatt gctggatgcg 900 ccctgaggac attgattacc cccgtcctgt atatgaatgt catagttgct ccgatcttgc 960 tgctgaaatg gctgctgctt tggcttcggc ttccatcgtt ttcaaagaca acaaagcata 1020 ctctcaaaag cttgtccatg gtgcccgaac actctttaag tttgctaggg atcaaagagg 1080 cagatatagt gctggtcgtt ctgaccctgc cctcttttat aattcctcaa gttactggga 1140 tgagtttgtt tggggtggag cctggttata ctatgccact gggaattcat cctatcttca 1200 gttagctact catcctaaac ttgccaagca tgctggtgct ttctggggtg gcccagatta 1260 tggtgttctt agctgggata ataagcttgc tggtgctcag gtgcttctga gccgattgag 1320 attgtttttg agtcctgggt atccatatga ggaaatattg agtacgtttc ataatcaaac 1380 cagcataatt atgtgctcat tccttccggt tttcactagc tttaatagaa caaaaggagg 1440 tttgattcag ttaaaccatg gaaggcctca gccactgcaa tacgtagtca atgcagcctt 1500 cttagccgcc ctatatagtg attatcttga tgctgctgat acacctggat ggtattgtgg 1560 tcccaatttc tattcaactg atgtcctgcg tgaatttgcc aaaacccaga ttgattatat 1620 ccttggcaaa aatcctcgaa aaatgagcta tgttgtgggc tttggtaacc attatccaaa 1680 gcatgttcac catagagggg catctatccc taagaataag atcaaatata actgtaaagg 1740 gggatggaaa tggagggata cgtcaaaacc aaaccccaac acacttgtgg gagccatggt 1800 agcaggacct gacaagcatg atgggtttcg tgatgttcgc accaactaca actatacgga 1860 gccaactcta gcaggcaacg cagggttggt tgctgcactc gtggcattgt ctggtgacaa 1920 ggcaaccgtg attgacaaga atactatttt ttctgcagtt ccaccaatgt ttcctacacc 1980 accaccactt ccggcacctt ggaaaccatg aaaacgtttt gatctttctt ctgtccatgt 2040 gtgacttaca gtctgatgat tttggaatta gtttttggta cgtaaatgac cttggaagtg 2100 taagtaacgc aaaaaggcaa gacaggagat gagtgatatg agacaacctg gacaaaactc 2160 gtggtgtttg gctgtcagat tggagagtca gagaagcatt caaacattga taatttgtat 2220 atgaagtcta tttggatttt gtggtataca gacagacgga gtgcatgtat gatattaatg 2280 ttgtattatt tgaaacacac caatatccat tgacaataaa tttgtgttta attgttgcag 2340 aaatctggcc tttgctatta ccaaaaaaaa aaaaaaaaaa ctcgag 2386 6 783 PRT Gossypium hirsutum 6 Ala Arg Ala Thr Leu Glu Asn Gln Arg Lys His His Cys Leu Leu Ile 1 5 10 15 His Ile Leu Phe Ile Lys Leu Asn Phe Leu Phe Val Leu Val Asp Gln 20 25 30 Ile Cys Arg Cys Ser Cys Ile Phe Arg Pro Leu Leu Phe Gln Ile Leu 35 40 45 Ile Met Tyr Gly Arg Asn Pro Trp Gly Gly Pro Leu Glu Ile Asn Ala 50 55 60 Thr Asp Ser Ala Thr Asp Asp Asp Arg Ser Arg Asn Leu Gln Asp Leu 65 70 75 80 Asp Arg Ala Ala Leu Ser Arg Pro Leu Asp Glu Thr Gln Gln Ser Trp 85 90 95 Leu Leu Gly Pro Gly Glu Gln Lys Lys Lys Lys Lys Tyr Val Asp Leu 100 105 110 Gly Cys Ile Ile Val Ser Arg Lys Ile Phe Val Trp Thr Val Gly Thr 115 120 125 Leu Leu Val Ser Ala Leu Leu Ala Gly Leu Ile Thr Leu Ile Val Lys 130 135 140 Thr Val Pro Arg His His His Arg His Ser Pro Pro Asp Asn Tyr Thr 145 150 155 160 Leu Ala Leu His Lys Ala Leu Met Phe Phe Asn Ala Gln Arg Ser Gly 165 170 175 Lys Leu Pro Lys His Asn Asn Val Ser Trp Arg Gly Asn Ser Gly Leu 180 185 190 Gln Asp Gly Lys Ser Asp Pro Ser Val Leu Met Lys Asp Leu Val Gly 195 200 205 Gly Tyr Tyr Asp Ala Gly Asp Ala Ile Lys Phe Asn Phe Pro Ala Ser 210 215 220 Phe Ser Met Thr Met Leu Ser Trp Ser Val Ile Glu Tyr Ser Ala Lys 225 230 235 240 Tyr Glu Ala Ala Gly Glu Leu Asn His Val Lys Glu Ile Ile Lys Trp 245 250 255 Gly Thr Asp Tyr Leu Leu Lys Thr Phe Asn Asn Thr Ala Asp Thr Ile 260 265 270 Asp Arg Ile Ala Ala Gln Val Gly Ile Gly Asp Thr Ser Gly Gly Val 275 280 285 Ser Ala Pro Asn Asp His Tyr Cys Trp Met Arg Pro Glu Asp Ile Asp 290 295 300 Tyr Pro Arg Pro Val Tyr Glu Cys His Ser Cys Ser Asp Leu Ala Ala 305 310 315 320 Glu Met Ala Ala Ala Leu Ala Ser Ala Ser Ile Val Phe Lys Asp Asn 325 330 335 Lys Ala Tyr Ser Gln Lys Leu Val His Gly Ala Arg Thr Leu Phe Lys 340 345 350 Phe Ala Arg Asp Gln Arg Gly Arg Tyr Ser Ala Gly Arg Ser Asp Pro 355 360 365 Ala Leu Phe Tyr Asn Ser Ser Ser Tyr Trp Asp Glu Phe Val Trp Gly 370 375 380 Gly Ala Trp Leu Tyr Tyr Ala Thr Gly Asn Ser Ser Tyr Leu Gln Leu 385 390 395 400 Ala Thr His Pro Lys Leu Ala Lys His Ala Gly Ala Phe Trp Gly Gly 405 410 415 Pro Asp Tyr Gly Val Leu Ser Trp Asp Asn Lys Leu Ala Gly Ala Gln 420 425 430 Val Leu Leu Ser Arg Leu Arg Leu Phe Leu Ser Pro Gly Tyr Pro Tyr 435 440 445 Glu Glu Ile Leu Ser Thr Phe His Asn Gln Thr Ser Ile Ile Met Cys 450 455 460 Ser Phe Leu Pro Val Phe Thr Ser Phe Asn Arg Thr Lys Gly Gly Leu 465 470 475 480 Ile Gln Leu Asn His Gly Arg Pro Gln Pro Leu Gln Tyr Val Val Asn 485 490 495 Ala Ala Phe Leu Ala Ala Leu Tyr Ser Asp Tyr Leu Asp Ala Ala Asp 500 505 510 Thr Pro Gly Trp Tyr Cys Gly Pro Asn Phe Tyr Ser Thr Asp Val Leu 515 520 525 Arg Glu Phe Ala Lys Thr Gln Ile Asp Tyr Ile Leu Gly Lys Asn Pro 530 535 540 Arg Lys Met Ser Tyr Val Val Gly Phe Gly Asn His Tyr Pro Lys His 545 550 555 560 Val His His Arg Gly Ala Ser Ile Pro Lys Asn Lys Ile Lys Tyr Asn 565 570 575 Cys Lys Gly Gly Trp Lys Trp Arg Asp Thr Ser Lys Pro Asn Pro Asn 580 585 590 Thr Leu Val Gly Ala Met Val Ala Gly Pro Asp Lys His Asp Gly Phe 595 600 605 Arg Asp Val Arg Thr Asn Tyr Asn Tyr Thr Glu Pro Thr Leu Ala Gly 610 615 620 Asn Ala Gly Leu Val Ala Ala Leu Val Ala Leu Ser Gly Asp Lys Ala 625 630 635 640 Thr Val Ile Asp Lys Asn Thr Ile Phe Ser Ala Val Pro Pro Met Phe 645 650 655 Pro Thr Pro Pro Pro Leu Pro Ala Pro Trp Lys Pro Lys Arg Phe Asp 660 665 670 Leu Ser Ser Val His Val Leu Thr Val Phe Trp Asn Phe Leu Val Arg 675 680 685 Lys Pro Trp Lys Cys Lys Arg Lys Lys Ala Arg Gln Glu Met Ser Asp 690 695 700 Met Arg Gln Pro Gly Gln Asn Ser Trp Cys Leu Ala Val Arg Leu Glu 705 710 715 720 Ser Gln Arg Ser Ile Gln Thr Leu Ile Ile Cys Ile Ser Leu Phe Gly 725 730 735 Phe Cys Gly Ile Gln Thr Asp Gly Val His Val Tyr Cys Cys Ile Ile 740 745 750 Asn Thr Pro Ile Ser Ile Asp Asn Lys Phe Val Phe Asn Cys Cys Arg 755 760 765 Asn Leu Ala Phe Ala Ile Thr Lys Lys Lys Lys Lys Lys Leu Glu 770 775 780 7 1179 DNA Gossypium hirsutum xyloglucan endoglycosyltransferase (XET) 7 ctcaaaccac cttgttctcc ccccttctcc gtctttctgg caacatgggt tcaccaccac 60 tttgggttct gcttctgggt gtgttgttta tggcttccgg aacaatcgca gctcccccta 120 agaagcctgt agatgtacca ttctccagaa actatatgcc tacttgggct tttgatcaca 180 ttaagtattt caatggtggc tctgacattc agctccacct tgacaaatac actggtactg 240 gtttccagtc caaaggatca tacttgttcg gacacttcag tatgcaaata aagctagtcc 300 ctggagattc tgctgggact gtcactgcct gttatttgtc ttctcaaaac tcagagcatg 360 atgagataga ttttgagttc ttgggcaaca gaacagggca accatacatt cttcagacca 420 atgtgttcac tggtggcaaa ggagacagag aacaaaggat ttacctttgg tttgacccaa 480 ccaaagaata ccactcctac tctgtcctct ggaacatgta tcagatantg ttctttgtgg 540 acgacatacc aatcagagtg ttcaaaaact gcaaagattt gggagtgagg tcaaggggtg 600 gtctcgaaaa gaccgactgg tccaaagccc cattcatagc cgcatacaag agcttccaca 660 tcgacgggtg cgagtcgtcg gtggaagcca agttctgcgc cacacaggga aagcggtggt 720 gggaccaaaa ggcattcgag gacctcgacg cctatcagtg gcgcagactg cgttgggtcc 780 gcaacaagtt cactatttac aactattgca gcgatagggt gaggtacccc acaatgtcgc 840 ccgagtgcaa gagagacaga gacgcttgag tcatttccat caccaccgag tcaattgctt 900 gttggccttc acttatttcc acatcaattt cattatatgt aatttcactc ctaaaacatt 960 tgttttcgtg ataatattat ttaaacatag attaccatct cttgacgggg gacaagacca 1020 tnatcttgta agtataagta taagaagctt gggattcgat ttcaagaaat nnaagtctat 1080 ttaaaaaaaa aaaaaaaaaa aactcgaggg ggggcccggt acccaattcc gccctatagt 1140 tgagtcctat acnattccac tgggccgtct ttttacaac 1179 8 274 PRT Gossypium hirsutum MOD_RES (162) Xaa = any amino acid 8 Met Gly Ser Pro Pro Leu Trp Val Leu Leu Leu Gly Val Leu Phe Met 1 5 10 15 Ala Ser Gly Thr Ile Ala Ala Pro Pro Lys Lys Pro Val Asp Val Pro 20 25 30 Phe Ser Arg Asn Tyr Met Pro Thr Trp Ala Phe Asp His Ile Lys Tyr 35 40 45 Phe Asn Gly Gly Ser Asp Ile Gln Leu His Leu Asp Lys Tyr Thr Gly 50 55 60 Thr Gly Phe Gln Ser Lys Gly Ser Tyr Leu Phe Gly His Phe Ser Met 65 70 75 80 Gln Ile Lys Leu Val Pro Gly Asp Ser Ala Gly Thr Val Thr Ala Cys 85 90 95 Tyr Leu Ser Ser Gln Asn Ser Glu His Asp Glu Ile Asp Phe Glu Phe 100 105 110 Leu Gly Asn Arg Thr Gly Gln Pro Tyr Ile Leu Gln Thr Asn Val Phe 115 120 125 Thr Gly Gly Lys Gly Asp Arg Glu Gln Arg Ile Tyr Leu Trp Phe Asp 130 135 140 Pro Thr Lys Glu Tyr His Ser Tyr Ser Val Leu Trp Asn Met Tyr Gln 145 150 155 160 Ile Xaa Phe Phe Val Asp Asp Ile Pro Ile Arg Val Phe Lys Asn Cys 165 170 175 Lys Asp Leu Gly Val Arg Ser Arg Gly Gly Leu Glu Lys Thr Asp Trp 180 185 190 Ser Lys Ala Pro Phe Ile Ala Ala Tyr Lys Ser Phe His Ile Asp Gly 195 200 205 Cys Glu Ser Ser Val Glu Ala Lys Phe Cys Ala Thr Gln Gly Lys Arg 210 215 220 Trp Trp Asp Gln Lys Ala Phe Glu Asp Leu Asp Ala Tyr Gln Trp Arg 225 230 235 240 Arg Leu Arg Trp Val Arg Asn Lys Phe Thr Ile Tyr Asn Tyr Cys Ser 245 250 255 Asp Arg Val Arg Tyr Pro Thr Met Ser Pro Glu Cys Lys Arg Asp Arg 260 265 270 Asp Ala 9 1695 DNA Artificial Sequence Description of Artificial Sequenceconsensus pectin methylesterase (PME) contig sequence 9 aaagcttttc ttggctctct ttgcgtcaat ccttcttgta actgccatag tcaccattgc 60 caccaccgtc tccatttcca aaaagaaatc cagtaatact gtagcagctc actccatcat 120 caaatcttca tgtagctcca cgttgtaccc agagttatgc tactcaacaa tctcttcagc 180 accagatgct gagaccaagg tcaagaaccc caaggatgtg attgaattgt cgttgaactt 240 gacggtgact gctgttcaga gtaactattt gtccatcaaa aagctcatta gtacccgaag 300 gaagagcctc acggagcgcg aaaaggctgc ccttaacgat tgtcttgaac tagtggatga 360 gactttggat gagctattcg tagctgaaca tgatctcagt gactatccaa gctttaacaa 420 gtcaatttcc caacatgctg atgaccttaa gagtcttctt agtgctgcaa tgaccaacca 480 agaaacttgc cttgatgggt tttctcacga taaagctgat aaaaaggtga ggcaagcgtt 540 gcttgacggg cagatgcatg tttttcatat gtgtagtaat gccctggcaa tgatcaagaa 600 cttgacggac acagacatgg caagccaagg ttatcatcca tcatctggga ggcaacttga 660 ggagcaagac caaacagaat ggcctaaatg gctgtcggag ggagatagga gactgttaca 720 ggctacaaca gtgattccta atgtaacagt ggccgctgat ggtagtggag acttcctcac 780 ggtgtctgag gcggtggcgg ctgcaccgga gagaagcacc acgaggtaca ttattaagat 840 taaagctgga gtttataggg aaacgtggat gtttccaagt aagaaaacca atctcatgtt 900 tgtgggagat gggagggtca acaccatcat cacagctagc agaaatgttg tcgatggcag 960 caccactttc cactctgcca ctgttgctgc ggtaggggac gggttcttgg ccagggatat 1020 aacatttcag aacacggctg gaccatcgaa gcaccaagca gtggcactgc gtgtgggctc 1080 tgatttatca gcattctaca ggtgtggcat tttagcatac caggacactc tctatgtcca 1140 cagccttcgc caattctatt cacaatgcct tgtagcaggc agcgtggact tcatattcgg 1200 aaatgcagca gcagtgttgc aagactgcga cattcatgct cgtcgaccca atccaaacca 1260 aaggaacatg gtcaccgcac aaggncgtag tgacccaaac gagaacactg ggattgtgat 1320 tcanaaatgt nggatcggtg caacctcgga tttagaagcc gttaaatccg attttgaaac 1380 ttatttaggg agaccatgga agacacattc gaagactgtt atcatgcaat ctgttataag 1440 tgatattatt catcctgctg gttggttccc atggggaaaa aaaattcgca ctcnaccttt 1500 gacgtatcng gaatatcana atactnggcc tggancttaa cncntcaanc agggttacat 1560 ggaaaagggt tattacntta tcccccacat atccggaagc ccaaaaccta cctgcctccg 1620 naatttttnt ttgggggaac ntaattgggt ttanccccnc cgggncttnc ctttccctcn 1680 tngaatcttt gaaaa 1695 10 521 PRT Gossypium hirsutum MOD_RES (1)..(521) Xaa = any amino acid 10 Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Lys Leu Phe Leu Ala Leu Phe 1 5 10 15 Ala Ser Ile Leu Leu Val Thr Ala Ile Val Thr Ile Ala Thr Thr Val 20 25 30 Ser Ile Ser Lys Lys Lys Ser Ser Asn Thr Val Ala Ala His Ser Ile 35 40 45 Ile Lys Ser Ser Cys Ser Ser Thr Leu Tyr Pro Glu Leu Cys Tyr Ser 50 55 60 Thr Ile Ser Ser Ala Pro Asp Ala Glu Thr Lys Val Lys Asn Pro Lys 65 70 75 80 Asp Val Ile Glu Leu Ser Leu Asn Leu Thr Val Thr Ala Val Gln Ser 85 90 95 Asn Tyr Leu Ser Ile Lys Lys Leu Ile Ser Thr Arg Arg Lys Ser Leu 100 105 110 Thr Glu Arg Glu Lys Ala Ala Leu Asn Asp Cys Leu Glu Leu Val Asp 115 120 125 Glu Thr Leu Asp Glu Leu Phe Val Ala Glu His Asp Leu Ser Asp Tyr 130 135 140 Pro Ser Phe Asn Lys Ser Ile Ser Gln His Ala Asp Asp Leu Lys Ser 145 150 155 160 Leu Leu Ser Ala Ala Met Thr Asn Gln Glu Thr Cys Leu Asp Gly Phe 165 170 175 Ser His Asp Lys Ala Asp Lys Lys Val Arg Gln Ala Leu Leu Asp Gly 180 185 190 Gln Met His Val Phe His Met Cys Ser Asn Ala Leu Ala Met Ile Lys 195 200 205 Asn Leu Thr Asp Thr Asp Met Ala Ser Gln Gly Tyr His Pro Ser Ser 210 215 220 Gly Arg Gln Leu Glu Glu Gln Asp Gln Thr Glu Trp Pro Lys Trp Leu 225 230 235 240 Ser Glu Gly Asp Arg Arg Leu Leu Gln Ala Thr Thr Val Ile Pro Asn 245 250 255 Val Thr Val Ala Ala Asp Gly Ser Gly Asp Phe Leu Thr Val Ser Glu 260 265 270 Ala Val Ala Ala Ala Pro Glu Arg Ser Thr Thr Arg Tyr Ile Ile Lys 275 280 285 Ile Lys Ala Gly Val Tyr Arg Glu Thr Trp Met Phe Pro Ser Lys Lys 290 295 300 Thr Asn Leu Met Phe Val Gly Asp Gly Arg Val Asn Thr Ile Ile Thr 305 310 315 320 Ala Ser Arg Asn Val Val Asp Gly Ser Thr Thr Phe His Ser Ala Thr 325 330 335 Val Ala Ala Val Gly Asp Gly Phe Leu Ala Arg Asp Ile Thr Phe Gln 340 345 350 Asn Thr Ala Gly Pro Ser Lys His Gln Ala Val Ala Leu Arg Val Gly 355 360 365 Ser Asp Leu Ser Ala Phe Tyr Arg Cys Gly Ile Leu Ala Tyr Gln Asp 370 375 380 Thr Leu Tyr Val His Ser Leu Arg Gln Phe Tyr Ser Gln Cys Leu Val 385 390 395 400 Ala Gly Ser Val Asp Phe Ile Phe Gly Asn Ala Ala Ala Val Leu Gln 405 410 415 Asp Cys Asp Ile His Ala Arg Arg Pro Asn Pro Asn Gln Arg Asn Met 420 425 430 Val Thr Ala Gln Xaa Arg Ser Asp Pro Asn Glu Asn Thr Gly Ile Val 435 440 445 Ile Xaa Lys Cys Xaa Ile Gly Ala Thr Ser Asp Leu Glu Ala Val Lys 450 455 460 Ser Asp Phe Glu Thr Tyr Leu Gly Arg Pro Trp Lys Thr His Ser Lys 465 470 475 480 Thr Val Ile Met Gln Ser Val Ile Ser Asp Ile Ile His Pro Ala Gly 485 490 495 Trp Phe Pro Trp Gly Lys Lys Ile Arg Thr Xaa Pro Leu Thr Tyr Xaa 500 505 510 Glu Tyr Xaa Asn Thr Xaa Pro Gly Xaa 515 520 11 33 PRT Artificial Sequence Description of Artificial Sequencededuced amino acid sequence from Gossypium hirsutum XET cDNA library 11 Val Ile Ser Ile Thr Thr Glu Ser Ile Ala Cys Trp Pro Ser Leu Ile 1 5 10 15 Ser Thr Ser Ile Ser Leu Tyr Val Ile Ser Leu Leu Lys His Leu Phe 20 25 30 Ser 12 18 PRT Artificial Sequence Description of Artificial Sequencededuced amino acid sequence from Gossypium hirsutum XET cDNA library 12 Tyr Tyr Leu Asn Ile Asp Tyr His Leu Leu Thr Gly Asp Lys Thr Xaa 1 5 10 15 Ile Leu 13 31 PRT Artificial Sequence Description of Artificial Sequencededuced amino acid sequence from Gossypium hirsutum XET cDNA library 13 Glu Ala Trp Asp Ser Ile Ser Arg Asn Xaa Ser Leu Phe Lys Lys Lys 1 5 10 15 Lys Lys Lys Asn Ser Arg Gly Gly Pro Val Pro Asn Ser Ala Leu 20 25 30 14 13 PRT Artificial Sequence Description of Artificial Sequencededuced amino acid sequence from Gossypium hirsutum XET cDNA library 14 Leu Ser Pro Ile Xaa Phe His Trp Ala Val Phe Leu Gln 1 5 10 15 52 PRT Artificial Sequence Description of Artificial Sequencededuced amino acid sequence for consensus PME contig sequence 15 Xaa Xaa Xaa Gln Gly Tyr Met Glu Lys Gly Tyr Tyr Xaa Ile Pro His 1 5 10 15 Ile Ser Gly Ser Pro Lys Pro Thr Cys Leu Xaa Asn Phe Xaa Leu Gly 20 25 30 Glu Xaa Asn Trp Val Xaa Pro Xaa Arg Xaa Xaa Pro Phe Pro Xaa Xaa 35 40 45 Ile Phe Glu Xaa 50 16 20 DNA Artificial Sequence Description of Artificial SequencePEPC2 PCR amplification primer COT189 16 ccatggatct ttgcctggac 20 17 19 DNA Artificial Sequence Description of Artificial SequencePEPC2 PCR amplification primer COT185 17 gcattccagc agcaatacc 19 18 12 PRT Artificial Sequence Description of Artificial SequencePEPC enzyme glycine-rich motif conserved region 18 Phe His Gly Arg Gly Gly Xaa Xaa Gly Arg Gly Gly 1 5 10 19 10 PRT Artificial Sequence Description of Artificial Sequenceconserved region containing Lys residue implicated in PEPC activity 19 Gly Tyr Ser Asp Ser Xaa Lys Asp Xaa Gly 1 5 10 20 7 PRT Artificial Sequence Description of Artificial Sequenceconserved region containing His residue essential for PEPC activity 20 Val Xaa Thr Ala His Pro Thr 1 5 21 11 PRT Artificial Sequence Description of Artificial SequenceN-terminal conserved region motif closely related to phosphorylation site 21 Xaa Xaa Xaa Xaa Ser Ile Asp Ala Gln Leu Arg 1 5 10 22 19 DNA Artificial Sequence Description of Artificial SequencePEPC1 quantitative RT-PCR clone-specific primer COT 285 22 ctttctgcgg agtacgaag 19 23 20 DNA Artificial Sequence Description of Artificial SequencePEPC1 quantitative RT-PCR clone-specific primer COT 288 23 cctgctctca tctcatcttg 20 

What is claimed is:
 1. An isolated nucleic acid molecule comprising a FE polynucleotide sequence, which is at least about 60% identical to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO: 5, SEQ ID NO: 7, or SEQ ID NO:
 9. 2. The isolated nucleic acid molecule of claim 1, wherein the isolated nucleic acid molecule comprises at least about 50 nucleotides in length.
 3. The isolated nucleic acid molecule of claim 1, wherein the isolated nucleic acid molecule comprises at least about 100 nucleotides.
 4. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid encodes a PEPcase polypeptide having a sequence of SEQ ID NO:2.
 5. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid encodes an expansin polypeptide having a sequence of SEQ ID NO:4.
 6. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid encodes an endoglucanase polypeptide having a sequence of SEQ ID NO:6.
 7. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid encodes an XET polypeptide having a sequence of SEQ ID NO:8.
 8. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid encodes a PME polypeptide having a sequence of SEQ ID NO:10.
 9. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid is a PEPcase polynucleotide as shown in SEQ ID NO:1.
 10. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid is an expansin polynucleotide as shown in SEQ ID NO:3.
 11. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid is an endoglucanase polynucleotide as shown in SEQ ID NO:5.
 12. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid is an XET polynucleotide as shown in SEQ ID NO:7.
 13. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid is a PME polynucleotide as shown in SEQ ID NO:9.
 14. The isolated nucleic acid molecule of claim 1, further comprising a plant promoter operably linked to the FE polynucleotide.
 15. The isolated nucleic acid molecule of claim 14, wherein the plant promoter is a tissue-specific promoter.
 16. The isolated nucleic acid molecule of claim 15, wherein the promoter is a fiber-specific promoter.
 17. The isolated nucleic acid molecule of claim 14, wherein the promoter is an inducible promoter.
 18. The isolated nucleic acid molecule of claim 14, wherein the FE polynucleotide is linked to the promoter in an antisense orientation.
 19. A transgenic plant comprising an expression cassette containing a plant promoter operably linked to a heterologous FE polynucleotide sequence, which is at least about 60% identical to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:9.
 20. The transgenic plant of claim 19, wherein the FE polynucleotide encodes an FE polypeptide.
 21. The transgenic plant of claim 20, wherein the FE polypeptide has an amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, or SEQ ID NO:10.
 22. The transgenic plant of claim 19, wherein the heterologous FE polynucleotide is linked to the promoter in an antisense orientation.
 23. The transgenic plant of claim 19, wherein the plant promoter is a tissue specific promoter.
 24. The transgenic plant of claim 23, wherein the promoter is a fiber-specific promoter.
 25. The transgenic plant of claim 24, wherein the promoter is a cotton fiber specific promoter.
 26. The transgenic plant of claim 19, wherein the FE polynucleotide has a nucleic acid sequence of SEQ ID NO:1.
 27. The transgenic plant of claim 19, wherein the FE polynucleotide has a nucleic acid sequence of SEQ ID NO:3.
 28. The transgenic plant of claim 19, wherein the FE polynucleotide has a nucleic acid sequence of SEQ ID NO:5.
 29. The transgenic plant of claim 19, wherein the FE polynucleotide has a nucleic acid sequence of SEQ ID NO:7.
 30. The transgenic plant of claim 19, wherein the FE polynucleotide has a nucleic acid sequence of SEQ ID NO:9.
 31. The transgenic plant of claim 19, wherein the plant is a member of the genus Gossypium.
 32. A method of modulating fiber quality in a plant, the method comprising introducing into the plant an expression cassette containing a plant promoter operably linked to a heterologous FE polynucleotide sequence, which is at least about 60% identical to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:9.
 33. The method of claim 32, wherein the heterologous FE polynucleotide encodes a FE polypeptide.
 34. The method of claim 33, wherein the FE polypeptide has an amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, or SEQ ID NO:10.
 35. The method of claim 32, wherein the heterologous FE polynucleotide is linked to the promoter in an antisense orientation.
 36. The method of claim 32, wherein the heterologous FE polynucleotide has a nucleic acid sequence of SEQ ID NO:1.
 37. The method of claim 32, wherein the plant promoter is a tissue specific promoter.
 38. The method of claim 37, wherein the promoter is a fiber specific promoter.
 39. The method of claim 38, wherein the promoter is a cotton fiber specific promoter.
 40. The method of claim 32, wherein the plant is a member of the genus Gossypium.
 41. The method of claim 32, wherein the expression cassette is introduced into the plant through a sexual cross. 